title: Identification of an intact ParaHox cluster with temporal colinearity but altered spatial colinearity in the hemichordate Ptychodera flava.
abstract: BACKGROUND
  ParaHox and Hox genes are thought to have evolved from a common ancestral ProtoHox cluster or from tandem duplication prior to the divergence of cnidarians and bilaterians. Similar to Hox clusters, chordate ParaHox genes including Gsx, Xlox, and Cdx, are clustered and their expression exhibits temporal and spatial colinearity. In non-chordate animals, however, studies on the genomic organization of ParaHox genes are limited to only a few animal taxa. Hemichordates, such as the Enteropneust acorn worms, have been used to gain insights into the origins of chordate characters. In this study, we investigated the genomic organization and expression of ParaHox genes in the indirect developing hemichordate acorn worm Ptychodera flava.
  
  
  RESULTS
  We found that P. flava contains an intact ParaHox cluster with a similar arrangement to that of chordates. The temporal expression order of the P. flava ParaHox genes is the same as that of the chordate ParaHox genes. During embryogenesis, the spatial expression pattern of PfCdx in the posterior endoderm represents a conserved feature similar to the expression of its orthologs in other animals. On the other hand, PfXlox and PfGsx show a novel expression pattern in the blastopore. Nevertheless, during metamorphosis, PfXlox and PfCdx are expressed in the endoderm in a spatially staggered pattern similar to the situation in chordates.
  
  
  CONCLUSIONS
  Our study shows that P. flava ParaHox genes, despite forming an intact cluster, exhibit temporal colinearity but lose spatial colinearity during embryogenesis. During metamorphosis, partial spatial colinearity is retained in the transforming larva. These results strongly suggest that intact ParaHox gene clustering was retained in the deuterostome ancestor and is correlated with temporal colinearity.
authors.affiliation: Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.
authors.forename: Tetsuro
authors.initials: T
authors.lastname: Ikuta
authors.forename: Yi-Chih
authors.initials: YC
authors.lastname: Chen
authors.forename: Rossella
authors.initials: R
authors.lastname: Annunziata
authors.forename: Hsiu-Chi
authors.initials: HC
authors.lastname: Ting
authors.forename: Che-huang
authors.initials: CH
authors.lastname: Tung
authors.forename: Ryo
authors.initials: R
authors.lastname: Koyanagi
authors.forename: Kunifumi
authors.initials: K
authors.lastname: Tagawa
authors.forename: Tom
authors.initials: T
authors.lastname: Humphreys
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.forename: Hidetoshi
authors.initials: H
authors.lastname: Saiga
authors.forename: Nori
authors.initials: N
authors.lastname: Satoh
authors.forename: Jr-Kai
authors.initials: JK
authors.lastname: Yu
authors.forename: Maria Ina
authors.initials: MI
authors.lastname: Arnone
authors.forename: Yi-Hsien
authors.initials: YH
authors.lastname: Su
mesh_terms: D000818:Animals; D002816:Chordata, Nonvertebrate / Q000145:classification / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D018398:Homeodomain Proteins / Q000235:genetics*; D005810:Multigene Family; D010802:Phylogeny
chemical_list: D018398:Homeodomain Proteins